Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

Abstract

BackgroundFinger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful.ResultsExperimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one half of the genome is repetitive in nature. The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the finger millet genome. Functional annotation and mining of transcription factors revealed finger millet genome harbors large number of drought tolerance related genes. Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding.ConclusionsThis genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3850-z) contains supplementary material, which is available to authorized users.

Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet

“…Whereas in other types, AGG & AAG in tri, AAAG in tetra and CGTCA in penta type were most frequent in rest of the species. These results were in accordance with the previous reports in finger millet and other major crops as the mining for repeats in genomic region yielded 39 to 66% of AG/CT repeats [9,13]. The comparative low number of di-nucleotide SSRs was attributed to the reason that these repeats were often present in close vicinity of other repeats, especially penta nucleotides forming compound SSRs.…”

“…The abundant presence of trinucleotide repeats when compared to other repeats has been reported in finger millet [19], but the recent genome-wide study has reported the presence of 58.5% of di-and 35.5% of tri-nucleotide repeats in finger millet genome [13]. However, di-nucleotide repeats were virtually absent in all the wild species except in few compound formats wherein they were found in close association along with other repeats (Figure 2).…”

“…Similarly, a set of 87 genomic SSRs when tested in Indian cultivars, were more informative than non-Indian cultivars by Ramakrishnan et al, [5]. The low success rate with ESTderived SSRs is the possible concern as it yields to occurrence of null alleles due to either variation in primer site / disruption of priming site by unrecognized intron splicing [21] and such issues with EST-SSRs can be easily addressed with the recent availability of genome sequence information in finger millet [13]. Further, unlike in other major crops, more and more systemic efforts are required in finger millet for molecular characterization of wild relatives and their utilization in trait improvement for biotic and abiotic stress tolerance [22].…”

“…However, the microsatellites derived from cultivated species were more informative than those derived from the wild types as they had higher polymorphic information content (PIC) value of 0.34 (average) as against 0.29. Hittalmani et al (2017) reported high polymorphism in wild species of finger millet than E. coracana germplasm with genomic SSRs derived from a cultivated finger millet variety.…”

“…However, the study further stresses on in-depth studies on wild relatives of E. coracana [13] for understanding its probable progenitors. One of the studies on genetic variation within Eleusine species using genomic SSRs indicate high intra-specific polymorphism among the cultivated africana (32%) and coracana (17%) species than wild species viz., E. intermedia, E. indica, E. multiflora, and E. floccifolia [14].…”